Analysis of the molecular networks in androgen dependent and independent prostate cancer revealed fragile and robust subsystems

PLoS ONE

Volumn 5, Issue 1, 2010, Pages

  Tasseff, Ryan ^a   Nayak, Satyaprakash ^a   Salim, Saniya ^a   Kaushik, Poorvi ^a   Rizvi, Noreen ^a   Varner, Jeffrey D ^a  

^a Cornell University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACID PHOSPHATASE PROSTATE ISOENZYME; ANDROGEN; ANDROGEN RECEPTOR; CYCLIN D; GROWTH FACTOR RECEPTOR; MITOGEN ACTIVATED PROTEIN KINASE 14; PROSTATE SPECIFIC ANTIGEN; PROTEIN KINASE B;

ANDROGEN ABLATION THERAPY; ARTICLE; CANCER GROWTH; CELL STRAIN LNCAP; DISEASE SIMULATION; GENETIC TRANSCRIPTION; HORMONAL REGULATION; HORMONAL THERAPY; HORMONE ACTION; HORMONE DEPENDENCE; HORMONE RESPONSE; HORMONE SENSITIVITY; MATHEMATICAL MODEL; METASTASIS; PROSTATE CANCER; PROTEIN EXPRESSION; RNA TRANSLATION; SENSITIVITY ANALYSIS; SIGNAL TRANSDUCTION; SIMULATION;

ANDROGENS; CELL LINE, TUMOR; CYCLIN D; HUMANS; MALE; PROSTATE-SPECIFIC ANTIGEN; PROSTATIC NEOPLASMS;

EID: 77749233793     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008864     Document Type: Article

References (85)

1. Jemal A, Siegel R, Ward E, Murray T, Xu J, et al. (2007) Cancer statistics, 2007. CA Cancer J Clin 57: 43-66.
2. Huggins C, Hodges CV (1941) Studies on prostatic cancer: I. the effect of castration, of estrogen and of androgen injection on serum phosphatases in metastatic carcinoma of the prostate. 1941. Cancer Research. pp 293-297.
3. Papsidero LD, Wang MC, Valenzuela LA, Murphy GP, Chu TM (1980) A prostate antigen in sera of prostatic cancer patients. Cancer Res 40: 2428-2432.
4. Kuriyama M, Wang MC, Lee CL, Killian CS, Papsidero LD, et al. (1982) Multiple marker evaluation in human prostate cancer with the use of tissue-specific antigens. J Natl Cancer Inst 68: 99-105.
5. Sadar MD, Hussain M, Bruchovsky N (1999) Prostate cancer: molecular biology of early progression to androgen independence. Endocr Relat Cancer 6: 487-502.
6. Eisenberger MA, Blumenstein BA, Crawford ED, Miller G, McLeod DG, et al. (1998) Bilateral orchiectomy with or without flutamide for metastatic prostate cancer. N Engl J Med 339: 1036-1042.
7. Tannock IF, de Wit R, Berry WR, Horti J, Pluzanska A, et al. (2004) Docetaxel plus prednisone or mitoxantrone plus prednisone for advanced prostate cancer. N Engl J Med 351: 1502-1512.
8. Evans RM (1988) The steroid and thyroid hormone receptor superfamily. Science 240: 889-895.
9. Carson-Junica MA, Schrader WT, O'Malley BW (1990) Sterioid receptor family: structure and functions. Endocr Rev 11: 201-220.
10. McConnell JD (1955) Prostatic growth: new insights into hormonal regulation. Br J Urol 76: 5-10.
11. Riegman PH, Vlietstra RJ, van der Korput JA, Brinkmann AO, Trapman J (1991) The promoter of the prostate-specific antigen gene contains a functional androgen responsive element. Mol Endocrinol 5: 1921-1930.
12. Gelmann EP (2002) Molecular biology of the androgen receptor. J Clin Oncol 20: 3001-3015.
13. Igawa T, Lin FF, Lee MS, Karan D, Batra SK, et al. (2002) Establishment and characterization of androgen-independent human prostate cancer lncap cell model. Prostate 50: 222-235.
14. Lee MS, Igawa T, Yuan TC, Zhang XQ, Lin FF, et al. (2003) Erbb-2 signaling is involved in regulating psa secretion in androgen-independent human prostate cancer lncap c-81 cells. Oncogene 22: 781-796.
15. Feldman BJ, Feldman D (2001) The development of androgen-independent cancer. Nature Rev Cancer 1: 34-45.
16. Culig Z, Hobisch A, Cronauer MV, Radmayr C, Trapman J, et al. (1994) Androgen receptor activation in prostatic tumor cell lines by insulin-like growth factor-i, keratinocyte growth factor, and epidermal growth factor. Cancer Res 54: 5474-5478.
17. Nazareth LV, Weigel NL (1996) Activation of the human androgen receptor through a protein kinase a signaling pathway. J Biol Chem 271: 19900-19907.
18. Yeh S, Lin HK, Kang HY, Thin TH, Lin MF, et al. (1999) From her2/neu signal cascade to androgen receptor and its coactivators: a novel pathway by induction of androgen target genes through map kinase in prostate cancer cells. Proc Natl Acad Sci U S A 96: 5458-5463.
19. Craft N, Shostak Y, Carey M, Sawyers CL (1999) A mechanism for hormone-independent prostate cancer through modulation of androgen receptor signaling by the her-2/neu tyrosine kinase. Nat Med 5: 280-285.
20. Meng TC, Lee MS, Lin MF (2000) Interaction between protein tyrosine phosphatase and protein tyrosine kinase is involved in androgen-promoted growth of human prostate cancer cells. Oncogene 19: 2664-2677.
21. Vihko P (1979) Human prostatic acid phosphatases: purification of a minor enzyme and comparisons of the enzymes. Invest Urol 16: 349-352.
22. Lin MF, Clinton GM (1988) The epidermal growth factor receptor from prostate cells is dephosphorylated by a prostate-specific phosphotyrosyl phosphatase. Mol Cell Biol 8: 5477-5485.
23. Sinha AA, Gleason DF, Wilson MJ, Wick MR, Reddy PK, et al. (1988) Relationship of prostatic acid phosphatase localization in human prostate by a monoclonal antibody with the gleason grading system. Prostate 13: 1-15.
24. Sakai H, Shiraishi K, Minami Y, Yushita Y, Kanetake H, et al. (1991) Immunohistochemical prostatic acid phosphatase level as a prognostic factor of prostatic carcinoma. Prostate 19: 265-272.
25. Meng TC, Lin MF (1998) Tyrosine phosphorylation of c-erbb-2 is regulated by the cellular form of prostatic acid phosphatase in human prostate cancer cells. J Biol Chem 273: 22096-22104.
26. Veeramani S, Yuan T, Chen S, Lin F, Petersen JE, et al. (2005) Cellular prostatic acid phosphatase: a protein tyrosine phosphatase involved in androgen-independent proliferation of prostate cancer. Endocrine-Related Cancer 12: 805-822.
27. Horoszewicz JS, Leong SS, Kawinski E, Karr JP, Rosenthal H, et al. (1983) Lncap model of human prostatic carcinoma. Cancer Res 43: 1809-1818.
28. Kholodenko BN, Demin OV, Moehren G, Hoek JB (1999) Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem 274: 30169-30181.
29. Huang CY, Ferrell JE (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci U S A 93: 10078-10083.
30. Computational modeling of the dynamics of the map kinase cascade activated by surface and internalized egf receptors. Nat Biotechnol 20: 370-375.
31. Vivanco I, Sawyers CL (2002) The phosphatidylinositol 3-kinase akt pathway in human cancer. Nat Rev Cancer 2: 489-501.
32. Richter JD, Sonenberg N (2005) Regulation of cap-dependent translation by eif4e inhibitory proteins. Nature 433: 477-480.
33. Fussenegger M, Bailey J, Varner J (2000) A mathematical model of caspase function in apoptosis. Nat Biotechnol 18: 768-774.
34. Schoeberl B, Eichler-Jonsson C, Gilles ED, Müller G (2002) Computational modeling of the dynamics of the map kinase cascade activated by surface and internalized egf receptors. Nat Biotechnol 20: 370-5.
35. Stelling J, Gilles ED, Doyle F Jr (2004) Robustness properties of circadian clock architectures. Proc Natl Acad Sci U S A 101: 13210-13215.
36. Queralt E, Lehane C, Novak B, Uhlmann F (2006) Downregulation of pp2a(cdc55) phosphatase by separase initiates mitotic exit in budding yeast. Cell 125: 719-732.
37. Li H, Ung CY, Ma XH, Liu XH, Li BW, et al. (2009) Pathway sensitivity analysis for detecting pro-proliferation activities of oncogenes and tumor suppressors of epidermal growth factor receptor-extracellular signal-regulated protein kinase pathway at altered protein levels. Cancer 115: 4246-4263.
38. Stites EC, Trampont PC, Ma Z, Ravichandran KS (2007) Network analysis of oncogenic ras activation in cancer. Science 318: 463-467.
39. Luan D, Zai M, Varner JD (2007) Computationally derived points of fragility of a human cascade are consistent with current therapeutic strategies. PLoS Comput Biol 3: e142.
40. Song SO, Varner J (2009) Modeling and analysis of the molecular basis of pain in sensory neurons. PLoS One 4: e6758.
41. Chen WW, Schoeberl B, Jasper PJ, Niepel M, Nielsen UB, et al. (2009) Inputoutput behavior of erbb signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol 5: 239.
42. Helmy M, Gohda J, Inoue JI, Tomita M, Tsuchiya M, et al. (2009) Predicting novel features of toll-like receptor 3 signaling in macrophages. PLoS One 4: e4661.
43. Selvarajoo K, Takada Y, Gohda J, Helmy M, Akira S, et al. (2008) Signaling flux redistribution at toll-like receptor pathway junctions. PLoS One 3: e3430.
44. Selvarajoo K, Tomita M, Tsuchiya M (2009) Can complex cellular processes be governed by simple linear rules? J Bioinform Comput Biol 7: 243-268.
45. Asthagiri AR, Lauffenburger DA (2001) A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (mapk) pathway model. Biotechnol Prog 17: 227-239.
46. Brown KS, Hill CC, Calero GA, Myers CR, Lee KH, et al. (2004) The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys Biol 1: 184-195.
47. Mayawala K, Gelmi CA, Edwards JS (2004) Mapk cascade possesses decoupled controllability of signal amplification and duration. Biophys J 87: L01-2.
48. Hornberg JJ, Binder B, Bruggeman FJ, Schoeberl B, Heinrich R, et al. (2005) Control of mapk signalling: from complexity to what really matters. Oncogene 24: 5533-5542.
49. Gadkar KG, Varner J, Doyle FJ (2005) Model identification of signal transduction networks from data using a state regulator problem. Syst Biol (Stevenage) 2: 17-30.
50. Gennemark P, Wedelin D (2009) Benchmarks for identification of ordinary differential equations from time series data. Bioinformatics 25: 780-786.
51. Bandara S, Schlöder J, Eils R, Bock HG, Meyer T (2009) Optimal Experimental Design for Parameter Estimation of a Cell Signaling Model. PLoS Comput Biol 5: e1000558.
52. Battogtokh D, Asch DK, Case ME, Arnold J, Schuttler HB (2002) An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of neurospora crassa. Proc Natl Acad Sci U S A 99: 16904-16909.
53. Kuepfer L, Peter M, Sauer U, Stelling J (2007) Ensemble modeling for analysis of cell signaling dynamics. Nat Biotech 25: 1001-1006.
54. Brown KS, Sethna JP (2003) Statistical mechanical approaches to models with many poorly known parameters. Phys Rev E Stat Nonlin Soft Matter Phys 68: 021904.
55. Palmer T, Shutts G, Hagedorn R, Doblas-Reyes F, Jung Y, et al. (2005) Representing model uncertainty in weather and climate prediction. Ann Rev Earth and Planetary Sci 33: 163-193.
56. Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, et al. (2007) Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 3: 1871-1878.
57. Lin MF, Lee MS, Garcia-Arenas R, Lin FF (2000) Differential responsiveness of prostatic acid phosphatase and prostate-specific antigen mrna to androgen in prostate cancer cells. Cell Biol Int 24: 681-689.
58. Kim J, Coetzee GA (2004) Prostate specific antigen gene regulation by androgen receptor. J Cell Biochem 93: 233-241.
59. Wilkinson MG, Millar JB (2000) Control of the eukaryotic cell cycle by map kinase signaling pathways. FASEB J 14: 2147-2157.
60. Barnes-Ellerbe S, Knudsen K, Puga A (2004) 2,3,7,8-tetrachlorodibenzo-p- dioxin blocks androgen-dependent cell proliferation of LNCaP cells through modulation of pRB phosphorylation. MOLECULAR PHARMACOLOGY 66: 502-511.
61. Eder I, Culig Z, Ramoner R, Thurnher M, Putz T, et al. (2000) Inhibition of LNCaP prostate cancer cells by means of androgen receptor antisense oligonucleotides. CANCER GENE THERAPY 7: 997-1007.
62. Aderem A (2005) Systems biology: its practice and challenges. Cell 121: 511-513.
63. Heinlein CA, Chang C (2004) Androgen receptor in prostate cancer. Endocr Rev 25: 276-308.
64. Igawa T, Lin FF, Rao P, Lin MF (2003) Suppression of lncap prostate cancer xenograft tumors by a prostate-specific protein tyrosine phosphatase, prostatic acid phosphatase. Prostate 55: 247-258.
65. Gao H, Ouyang X, Banach-Petrosky WA, Gerald WL, Shen MM, et al. (2006) Combinatorial activities of akt and b-raf/erk signaling in a mouse model of androgen-independent prostate cancer. Proc Natl Acad Sci U S A 103: 14477-14482.
66. Ziada A, Barqawi A, Glode LM, Varella-Garcia M, Crighton F, et al. (2004) The use of trastuzumab in the treatment of hormone refractory prostate cancer; phase ii trial. Prostate 60: 332-337.
67. Canil CM, Moore MJ, Winquist E, Baetz T, Pollak M, et al. (2005) Randomized phase ii study of two doses of gefitinib in hormone-refractory prostate cancer: a trial of the national cancer institute of canada-clinical trials group. J Clin Oncol 23: 455-460.
68. Soni A, Akcakanat A, Singh G, Luyimbazi D, Zheng Y, et al. (2008) eif4e knockdown decreases breast cancer cell growth without activating akt signaling. Mol Cancer Ther 7: 1782-1788.
69. Nayak S, Salim S, Luan D, Zai M, Varner JD (2008) A test of highly optimized tolerance reveals fragile cell-cycle mechanisms are molecular targets in clinical cancer trials. PLoS ONE 3: e2016.
70. Lukas J, Bartkova J, Bartek J (1996) Convergence of mitogenic signalling cascades from diverse classes of receptors at the cyclin d-cyclin-dependent kinase-prb-controlled g1 checkpoint. Mol Cell Biol 16: 6917-6925.
71. Burd CJ, Petre CE, Morey LM, Wang Y, Revelo MP, et al. (2006) Cyclin d1b variant influences prostate cancer growth through aberrant androgen receptor regulation. Proc Natl Acad Sci U S A 103: 2190-2195.
72. Yu Q, Geng Y, Sicinski P (2001) Specific protection against breast cancers by cyclin d1 ablation. Nature 411: 1017-1021.
73. Transcriptional profiling identifies cyclin d1 as a critical downstream effector of mutant epidermal growth factor receptor signaling. Cancer Res 66: 11389-11398.
74. Xu Y, Chen SY, Ross KN, Balk SP (2006) Androgens induce prostate cancer cell proliferation through mammalian target of rapamycin activation and post-transcriptional increases in cyclin d proteins. Cancer Res 66: 7783-92.
75. Bianco R, Shin I, Ritter CA, Yakes FM, Basso A, et al. (2003) Loss of pten/ mmac1/tep in egf receptor-expressing tumor cells counteracts the antitumor action of egfr tyrosine kinase inhibitors. Oncogene 22: 2812-2822.
76. Nagata Y, Lan KH, Zhou X, Tan M, Esteva FJ, et al. (2004) Pten activation contributes to tumor inhibition by trastuzumab, and loss of pten predicts trastuzumab resistance in patients. Cancer Cell 6: 117-127.
77. Sampson ER, Yeh SY, Chang HC, Tsai MY, Wang X, et al. (2001) Identification and characterization of androgen receptor associated coregulators in prostate cancer cells. J Biol Regul Homeost Agents 15: 123-129.
78. Hu YC, Yeh S, Yeh SD, Sampson ER, Huang J, et al. (2004) Functional domain and motif analyses of androgen receptor coregulator ara70 and its differential expression in prostate cancer. J Biol Chem 279: 33438-33446.
79. Balk SP, Knudsen KE (2008) Ar, the cell cycle, and prostate cancer. Nucl Recept Signal 6: e001.
80. de Souza PL, Russell PJ, Kearsley J (2009) Role of the akt pathway in prostate cancer. Curr Cancer Drug Targets 9: 163-175.
81. Los M, Maddika S, Erb B, Schulze-Osthoff K (2009) Switching akt: from survival signaling to deadly response. Bioessays 31: 492-495.
82. (2006) Expression and nuclear localization of erbb3 in prostate cancer. Clin Cancer Res 12: 2730-2737.
83. Cardillo MR, Monti S, Silverio FD, Gentile V, Sciarra F, et al. (2003) Insulinlike growth factor (igf)-i, igf-ii and igf type i receptor (igfr-i) expression in prostatic cancer. Anticancer Res 23: 3825-3835.
84. Tam L, McGlynn LM, Traynor P, Mukherjee R, Bartlett JMS, et al. (2007) Expression levels of the jak/stat pathway in the transition from hormonesensitive to hormone-refractory prostate cancer. Br J Cancer 97: 378-383.
85. Dickinson RP, Gelinas RJ (1976) Sensitivity analysis of ordinary differential equation systems - a direct method. J Comp Phys 21: 123-143.